GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gltX in Pseudomonas putida KT2440

Align glutamyl-tRNAGlx synthetase (EC 6.1.1.17; EC 6.1.1.24) (characterized)
to candidate PP_1977 PP_1977 Glutamate--tRNA ligase

Query= metacyc::MONOMER-13959
         (483 letters)



>FitnessBrowser__Putida:PP_1977
          Length = 493

 Score =  330 bits (847), Expect = 5e-95
 Identities = 175/479 (36%), Positives = 279/479 (58%), Gaps = 16/479 (3%)

Query: 5   VRVRYAPSPTGHLHIGNARTALFNYLFARNQGGKFIIRVEDTDKKRNIEGGEQSQLNYLK 64
           VR R APSPTG  H+G A  ALFNY FA+  GG+FI+R+EDTD+ R+    EQ   + L+
Sbjct: 4   VRTRIAPSPTGDPHVGTAYIALFNYCFAKQHGGEFILRIEDTDQLRSTRESEQQIFDALR 63

Query: 65  WLGIDWDESVDVGGEYGPYRQSERNDIYKVYYEELLEKGLAYKCYCTEEELEKEREEQIA 124
           WLGI+W+E  DVGG +GPYRQSER +IY  Y +EL++ G A+ C+CT EELE+ R EQ A
Sbjct: 64  WLGIEWNEGPDVGGPHGPYRQSERGEIYAKYAKELVDAGHAFYCFCTAEELEQMRAEQQA 123

Query: 125 RGEMPRYSGKHRDLTQEEQEKFIAEGRKPSIRFRVPEGKVIAFNDIVKGEISFESDGIGD 184
           RGE PRY G+   ++ EE ++ +  G    IR +VP   +    D+++G++    D +  
Sbjct: 124 RGETPRYDGRALLMSAEEVQRRLDAGEPHVIRMKVPSEGICVVPDMLRGDVEIPWDRMDM 183

Query: 185 FVIVKKDGTPTYNFAVAIDDYLMKMTHVLRGEDHISNTPKQIMIYQAFGWDIPQFGHMTL 244
            V++K DG PTY  A  +DD+LM +THVLRGE+ + + PK I +Y+ FGW+ P+  +M L
Sbjct: 184 QVLMKNDGLPTYFLANVVDDHLMGITHVLRGEEWLPSAPKLIKLYEYFGWEQPKLCYMPL 243

Query: 245 IVNESRKKLSKRDESIIQFIEQYKELGYLPEALFNFIGLLGWSPVGEEELFTKEQFIEIF 304
           + N  + KLSKR       +  Y+ +G++PEA+ N++G +GWS   E E F+  + +E F
Sbjct: 244 LRNPDKSKLSKRKNP--TSVTFYERMGFMPEAMLNYLGRMGWSMPDEREKFSLAEMVEHF 301

Query: 305 DVNRLSKSPALFDMHKLKWVNNQYVKKLDLDQVVELTLPHLQKAGKVGTELSAEEQEWVR 364
           D++R+S    +FD+ KL W+N Q++++L +++        LQK         A   +++ 
Sbjct: 302 DLSRISLGGPIFDIEKLSWLNGQWLRELPVEEFA----ARLQK--------WAFNSDYMM 349

Query: 365 KLISLYHEQLSYGAEIVELTDLFFTDEIEYNQE--AKAVLEEEQVPEVLSTFAAKLEELE 422
           K+      ++   +++  L   FF   ++ + +      L  +QV +V+     KLE L 
Sbjct: 350 KIAPHVQGRVETFSQVAPLGGFFFEGALKLDAKLFESKKLSADQVRQVIQLILWKLESLR 409

Query: 423 EFTPDNIKASIKAVQKETGHKGKKLFMPIRVAVTGQTHGPELPQSIELIGKETAIQRLK 481
           ++  + I   I+AV +    K +     +  A+TGQ     +  ++E++G +    RL+
Sbjct: 410 QWEKERITGCIQAVVEALELKLRDAMPLMFAAITGQASSVSVLDAMEILGPDLTRYRLR 468


Lambda     K      H
   0.316    0.137    0.394 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 637
Number of extensions: 29
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 483
Length of database: 493
Length adjustment: 34
Effective length of query: 449
Effective length of database: 459
Effective search space:   206091
Effective search space used:   206091
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 52 (24.6 bits)

This GapMind analysis is from Aug 03 2021. The underlying query database was built on Aug 03 2021.

Links

Downloads

Related tools

About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory